4F31: Kainate

Kainate bound to the D655A mutant of the ligand binding domain of GluA3. Determined by X-ray diffraction at 2.29 Å resolution. Released 30 May 2012.

Method: X-ray diffraction
Resolution: 2.29 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 4,328
Mol. weight: 58.54 kDa
Ligands: KAI, ZN
Released: 30 May 2012

Explore 4F31 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F31 contains 29 α-helices and 41 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	1
β-strand	13	1	2
β-strand	17	1	2
β-strand	18-19	2	3
α-helix	23-25	3
α-helix	28-31	4
β-strand	32-33	2	3
α-helix	35-47	13
β-strand	50-55	6	1
β-strand	64	1	4
β-strand	71	1	4
α-helix	73-79	7
β-strand	85-86	2	1
β-strand	91	1	5
α-helix	94-97	4
β-strand	100-102	3	1
β-strand	107-109	3	5
β-strand	111-116	6	6
α-helix	124-128	5
β-strand	134	1	7
β-strand	138	1	8
α-helix	142-149	8
α-helix	153-164	12
β-strand	171	1	8
α-helix	174-183	10
β-strand	188	1	7
β-strand	191-193	3	6
α-helix	194-201	8
β-strand	208-211	4	6
β-strand	218-220	3	5
β-strand	223-225	3	1
α-helix	231-243	13
α-helix	246-251	6
α-helix	252-257	6

Chain D: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6-10	5	9
β-strand	13	1	10
β-strand	17	1	10
β-strand	18-19	2	11
α-helix	23-25	3
α-helix	28-31	4
β-strand	32-33	2	11
α-helix	35-46	12
β-strand	51-55	5	9
β-strand	64	1	12
β-strand	71	1	12
α-helix	73-80	8
β-strand	85-86	2	9
β-strand	91	1	13
α-helix	94-99	6
β-strand	100-102	3	9
α-helix	103	1
α-helix	105	1
β-strand	107-109	3	13
β-strand	111-116	6	14
α-helix	124-128	5
β-strand	134-136	3	14
β-strand	138	1	15
α-helix	142-149	8
α-helix	153-164	12
β-strand	171	1	15
α-helix	174-183	10
β-strand	188-193	6	14
α-helix	194-201	8
β-strand	208-211	4	14
β-strand	218-220	3	13
β-strand	223-225	3	9
α-helix	229-243	15
α-helix	246-251	6
α-helix	252-256	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 3	B, D	protein	258	Rattus norvegicus	P19492 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>4F31_1 Glutamate receptor 3 (chains B, D)
RTIVVTTILESPYVMYKKNHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGA
RDPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKGTPIES
AEDLAKQTEIAYGTLASGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRK
SKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGNAVNLAVLKLNE
QGLLDKLKNKWWYDKGEC

Ligands and cofactors

ID	Name	Formula	Copies
KAI	3-(carboxymethyl)-4-isopropenylproline	C10 H15 N O4	2
ZN	Zinc ion	Zn	4

Primary citation

The loss of an electrostatic contact unique to AMPA receptor ligand binding domain 2 slows channel activation. Holley, S.M., Ahmed, A.H., Srinivasan, J. et al. Biochemistry (2012) 51:4015-4027. DOI 10.1021/bi3001837 · PubMed

Other PDB entries of the same protein (UniProt P19492 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4F29 1.75 Å, Quisqualate bound to the ligand binding domain of GluA3i
3LSW 1.75 Å, Aniracetam bound to the ligand binding domain of GluA3
4F1Y 1.79 Å, CNQX bound to the ligand binding domain of GluA3
3M3K 1.79 Å, Ligand binding domain (S1S2) of GluA3 (flop)
4F3B 1.82 Å, Glutamate bound to the D655A mutant of the ligand binding domain of GluA3
4F39 1.83 Å, Kainate bound to the ligand binding domain of GluA3
3DLN 1.91 Å, Crystal structure of the binding domain of the AMPA subunit GluR3 bound to glutamate
4F2O 1.91 Å, Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3
6FPJ 1.96 Å, Structure of the AMPAR GluA3 N-terminal domain bound to phosphate
3LSX 2.01 Å, Piracetam bound to the ligand binding domain of GluA3
4F22 2.06 Å, Kainate bound to the K660A mutant of the ligand binding domain of GluA3
4F3G 2.06 Å, Kainate bound to the ligand binding domain of GluA3i

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